Mice bearing the mutant gene Cat:Fr have dominantly inherited congenital cataracts, which are more extensive in the mutant homozygote than in the heterozygote. The biochemical and ultrastructural properties of these lenses were examined and compared with those of lenses in which cataracts were induced with acetaminophen and bleomycin. The Cat mutation induces a dominant, by inheritance, loss of beta-H crystallins, but this change is also seen in the bleomycin cataracts, and in the presence of 1 M sucrose, or at 4(DEGREES)C. There are codominantly inherited alterations in the relative proportions of crystallin and albuminoid components in the inherited cataracts, and in the presence of 1 M sucrose. Changes in amino acid composition of the lens proteins are dominantly inherited in the Cat mutation. There are also abnormalities of amino acid composition in the proteins from the acetaminophen cataracts, but these are different from those caused by the mutation. As to the ultrastructural changes, the inherited cataracts have a relatively normal anterior epithelium, but show marked degeneration of nuclear and deep cortical fibres. The bleomycin cataracts also show extensive nuclear destruction, but in addition, appear to be completely devoid of capsule, and have degenerating anterior epithelium cells, which are not seen in the inherited cataract. The acetaminophen cataracts, by contrast, retain normal overall structural architecture, but the individual fibres become swollen and flaky, and develop an increased number of interdigitating processes. These abnormal biochemical properties not unique to the Cat:Fr mouse are unlikely to be proximal effects of the mutant gene, and may be general consequences of the presence of a cataract, from whatever cause. The differences between ultrastructural abnormalities seen in the drug induced and inherited cataracts suggest that these etiological agents induce cataracts by different mechanisms, a fact that is not always apparent from

Bibliography: leaves 218-251 / xviii, [ca. 100] leaves : ill ; 31 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Microbiology and Immunology, 1983

Some ill. mounted / Bibliography: leaves 109-129 / xiii, 129, [ca. 60] leaves : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Microbiology and Immunology, 1984

M.A. / Two species of multimammate mouse, Mastomys coucha and M. natalensis are common, and widely distributed in southern Africa, occurring sympatrically in some areas, and allopatrically in others. The limits of their distribution are only provisional so far. As they share a high degree of morphological similarity, they are, as yet, impossible to identify with certainty in the field. Each species of multimammate mouse carries important diseases: with M. coucha being a carrier for the bacterium causing plague, and M. natalensis carrying the virus causing Lassa fever. In many areas, multimammate mice, being highly adaptable and ecological generalists, have become co-habitants with humans. This fact, coupled to the medical significance of both species, lends importance to being able to identify each species where it occurs, especially in areas where they occur sympatrically. Thus, a total of 40 specimens of M. natalensis were trapped from Richards Bay and La Lucia ridge in KwaZulu-Natal, and 43 specimens of M. coucha from Montgomery Park in Johannesburg and from the shores of the Vaal Dam in the Free State with the aim of comparing these two species via gel electrophoresis. These specimens were from allopatric populations from the centres of their provisional distributions. It was expected that there would be genetic differences between the two sibling species. Blood, liver, and muscle samples were taken, either in the field from dead specimens caught in snap-traps, or back in the laboratory from live-trapped specimens. Fifteen proteins or enzymes provided interpretable results at a total of 39 loci. Nineteen of these were polymorphic

It is submitted in this thesis that the degree of activation or inhibition of macrophage function may differ in N. asteroides and N. brasiliensis infections with respect to release of plasminogen activator and of lysozyme The pattern of secretion of plasminogen activator and lysozyme in N. asteroides infections appears to differ in N. brasiliensis infection; and there is possibly a difference in the amount of lysozyme released by 2 day N. asteroides-activated macrophages and 2 day N. brasiliensis -activated macrophages. Strains of Nocardia organism did not influence macrophage morphology or ultrastructure. The study also shows the biochemical characteristics of plasminogen activator and lysozyme release, but not macrophage morphology and ultrastructure, are modified in the first 21 days of experimental Nocardia infections. There are three apparent mechanisms by which virulent strains of N. asteroides manage to survive within macrophages: (i) an ability to inhibit phagosome-lysozome fusion: (ii) alteration in the intraphagosomal pH: and (iii) alteration in the activity of the lysozomal enzyme acid-phosphatase. This study attempted to elucidate further the mechanisms enabling Nocardia organisms to persist and grow within macrophages. Reduced lysozyme release reflects diminished functional status of the macrophages of mice inoculated with N. asteroides or N. brasiliensis at certain times during infection. Reduced intracellular lysozyme levels have been linked with defects in bactericidal function. Such a reduction in intracellular and consequently extracellular levels of lysozyme might explain the capacity of Nocardia to survive intracellularly and to proliferate in the macrophage host.

Pancreatic cancer is the 10th most common cancer diagnosis and 4th most common cause of cancer mortality in the United States, highlighting a disparity between disease prevalence and outcome. Ineffective drug delivery to these tumors contributes to the poor prognosis for this disease, as intravenous drug delivery is hampered by poor vascularity within these tumors. Bacterial therapy, or the use of bacterial components to treat disease, is thought to be able to overcome such drug delivery challenges; through a combination of tumor homing and long-term colonization, bacteria can be utilized to produce anti-cancer molecules directly within the cores of tumors. As such, here, we interrogate the feasibility of bacterial cancer therapy for pancreatic ductal adenocarcinoma (PDAC). Before delving too deeply into bacterial therapy design, it was important to first address one major limitation in therapeutic screening models. As a therapeutic should be effective against the entirety of the tumor, without a specific emphasis on the malignant epithelia, we developed and characterized a novel protocol for culturing ex vivo (explant) murine PDAC tissue with a corresponding protocol for human PDAC tissue. We demonstrated that these tumor slice explants retain the complex cellular architecture and population complexity throughout culture, making them a useful resource for not only therapeutic screens, but also paracrine interactions, which are infeasible to explore with in vitro and in vivo models. Use of these murine and human PDAC explant models assisted in the selection of a potent, bacterial-derived cytotoxin, theta toxin, as a potential therapeutic candidate for PDAC, in both bacteria lysate and live bacteria contexts. Ultimately, we employed a strain of a probiotic bacteria, E. coli Nissle 1917, as a ‘living drug’ to selectively produce theta toxin within the confines of a PDAC tumor in a mouse model of pancreatic cancer. In in vivo studies, we demonstrated that live bacteria preferentially colonize tumor tissue following a single, direct, intratumoral injection into the primary PDAC tumor. We found that not only did the bacteria colonize the injected tumor, but also translocated to distant regions of metastasis and secondary tumors such as anogenital papillomas. However, the long-term efficacy of this strategy is in question, as bacterial colonization and therapeutic capability waned after several weeks. Despite the limited time scale of the bacterial colonization, treatment with a single dose of live, theta toxin-producing bacteria provided a nearly 3-fold improvement in overall survival compared to vehicle and standard of care chemotherapy (gemcitabine) treatment arms. Preliminary evidence suggests that this improvement is due to a combination of the direct cytotoxic effect of the theta toxin and an inherently immunostimulatory capacity of these bacteria, resulting in an influx of anti-tumor immune cells and an overall reduction in immunosuppression phenotype markers. These findings suggest that bacterial therapy could be a useful tool for the treatment of pancreatic cancer, not solely due to the direct cytotoxic effect on the tumor, but with the potential for a combination treatment with immunotherapies.

The gastrointestinal (GI) tract is a crucial interface for the host, food derived antigens, the commensal microbiota and invasive pathogens. Here, the immune system must simultaneously protect against harmful pathogens and remain tolerogenic to commensal bacteria and nutrients. The intestinal mucosa of adult humans and mice is enriched for innate lymphoid cells (ILCs) that express the transcription factor RORγt (ILC3s). These cells are crucial for maintaining the delicate balance of tolerance and immunity in the GI tract. They serve protective roles in immune responses to infectious organisms, are essential for the formation of lymphoid tissues, and help maintain gut homeostasis via signaling to epithelial cells through interleukin 22 (IL-22). ILC3s in the GI tract can be further categorized into three main subsets with distinct and overlapping functional roles. These subsets can be identified by either the expression of CCR6, Nkp46, or by lacking both markers- double negative (DN), some of which also make IL-17A. Signals that mediate the development and function of the various ILC3 subsets are still an area of active investigation. Notch signaling is a highly conserved pathway that contributes to the development and function of many types of immune cells. There has been some investigation into the role Notch signaling plays in the development of ILC3, particularly in the transition from DN to Nkp46 ILC3. However, all three subsets of ILC3s express two Notch receptor isoforms (Notch1 and Notch2) the individual roles of these two receptors have not been dissected. We show signaling through Notch1 and Notch2 individually contribute to Nkp46 ILC3 development in a cell intrinsic manner. We also show Notch signaling, primarily through Notch2, reinforces the ILC3 program and suppresses the ILC1-like program in Nkp46 ILC3 by promoting the expression of RORγt, c-Maf, and IL-22, and suppressing the expression of T-bet and IFNγ. Notch signaling also supports ILC3-identity genes in CCR6 ILC3, promoting RORγt, IL-17A, and IL-22. We, therefore, identify a novel role for Notch signaling in ILC3 function. As such, Notch-deficient ILC3 fail to initiate proper immune response to enteric pathogen Citrobacter rodentium, leading to more severe infection. Our results show how a highly conserved signaling pathway contributes to ILC3 development, identity, and function. The GI tract is also enriched with helper CD4 T cells that express RORγt, IL-17A, and IL-22 (Th17), which share many phenotypic and functional features with ILC3. The relative contribution of ILC3 and Th17 cells to immune phenotypes remains poorly understood. Moreover, due to the lack of ILC3-specific depletion models, how ILC3 regulate mucosal protection in the presence of Th17 cells is not clear. Here, we examined non-redundant functions of ILC3 in intestinal immunity using novel ILC3-deficient mice that maintain endogenous T cells, Th17 cells, and secondary lymphoid organs. ILC3 depletion did not affect IL-22-production by CD4 T cells during homeostasis. However, despite the presence of IL-22-producing T cells, ILC3 and ILC3- derived IL-22 were required for maintaining homeostatic functions of the intestinal epithelium. ILC3 were dispensable for generation of Th17 and Th22 cell responses to pathogenic bacteria, though Th17 and Th22 responses were delayed in the absence of ILC3. ILC3- deficient mice were capable of pathogen clearance and survived infection with low dose Citrobacter rodentium in the presence of antigen-specific Th17 cells. However, ILC3 increased pathogen tolerance at early timepoints of infection by activating tissue-protective immune pathways. Consequently, ILC3 were indispensable for survival of high dose infection. We also assess the role of ILC3 and Th17 cell in metabolic syndrome, using our novel model. Our lab demonstrated commensal-specific Th17 cells are protective against metabolic syndrome and lost under high-fat, high-sugar diet. ILC3s drive the expansion of a commensal member, Faecalibaculum rodentium (F. rod), which displaces the Th17 cell-inducing commensal, segemented filamentous bacteria (SFB). Without ILC3s, SFB is not lost from the microbiota, commensal- specific Th17 cells are maintained and there is, therefore, no development of metabolic syndrome. Our results demonstrate crucial context- dependent roles for ILC3 in immune-sufficient animals during homeostasis, infection, and metabolic disease.

One of the most challenging questions in the study of cancer is the origin and the nature of the cells that initiate cancer. Accumulated studies have provided many molecular origins of cancers but we still do not know what kind of cells in the tissues transform to cancer cells. Therefore, identifying the cellular origin of these cells is critical for the development of better prognosis, diagnosis and treatment of cancer. A stem cell origin of cancer has been postulated over 150 years. Recent cancer stem cell studies have opened a new window on aspects of the cellular origin of cancer. In this communication, we will address two possible cellular origins of cancer in epithelial tumor development using mouse skin cancer model: tissue specific stem cells, and cells from other organs. To demonstrate contribution of the tissue specific stem cells in tumor development, we monitored the contribution of keratin-15 positive hair follicle bulge stem cells to skin tumor development in the multistage skin carcinogenesis model with Krtl- 15CrePRl;R26R transgenic mice. We found that labeled progeny of the keratin-15 positive bulge stem cells migrate into papillomas and these cells contribute to almost all papilloma samples by 20 weeks of promotion. Additionally, in contrast to the transient contribution of bulge-derived cells in skin wound healing, consistent percentage of the bulge-derived cells stay in the papillomas over 20 weeks. Furthermore, papillomas have heterogeneous expression of the codon 61 signature Ha-ras mutation, with approximately 30 percent of bulge-derived regions expressing the mutation. To determine the contribution of exogenous sources in skin tumor development, we examined bone marrow-derived cells (BMDCs) in the skin tumors from the allogeneic gender-mismatched bone marrow transplantation recipient mice after chemical skin carcinogenesis. We observed that genetically marked (EGFP) BMDCs were detected in the epithelial part of skin wounds and also skin tumors, and we found greater degree of BMDC contribution in chronic ulcer-related skin lesions. Lastly, an in-vitro assay demonstrated plasticity of BMDCs by inducing keratin-14 expressing cells from mesenchymal stem cells. These results demonstrated that hair follicle bulge stem cells and also BMDCs are able to contribute to skin tumor development.

Diseases of the aorta rank as the 20th leading cause of mortality in the US, contributing to 10,000 deaths annually. Thoracic aortic aneurysms are typically asymptomatic, often undetected until life-threatening aortic dissection or rupture occurs. Familial cases constitute one in five instances of thoracic aortic aneurysm and dissection (TAAD), with genetic causes being heterogeneous and known risk genes explaining only a small fraction of cases. We hypothesized that additional TAAD risk genes remain undiscovered. This thesis aims to investigate the genetic etiology of TAAD using genetic and genomic approaches. Our methodological approach included: 1) exome sequencing of DNA from TAAD patients with subsequent genomic analysis, integrating clinical data, and 2) single-cell RNA sequencing (scRNA-seq) of the developing (embryonic) mouse aorta. We sequenced 1650 DNA samples from 1429 TAAD patients and, after quality control, analyzed genomic data from 1278 unrelated TAAD patients of European ancestry. For controls, we used 145,103 unrelated individuals of European ancestry from the UK BioBank. We conducted a per-gene and per-domain burden analysis using a binomial test. To improve the power of detection of novel risk genes, we integrated case-control association of rare damaging variants with cell-type specific gene expression data from scRNA-seq of the ascending and descending aorta of 17 mouse embryos (harvested at the E15 stage) with the hypothesis that true risk genes are highly expressed early in development. Our analysis of known TAAD risk genes identified 52 pathogenic or likely pathogenic variants, explaining 4.1% of TAAD cases, and 75 variants of uncertain significance (5.9%). Next, two potential novel candidate genes emerged from the unbiased case-control analysis, which utilized AlphaFold domain-based annotation of protein structure: β-propeller domain of VPS8 (p = 8.8 × 10-9) and UTP11 (p = 3.9 × 10-8). scRNA-seq of the developing mouse aorta revealed significant cell-type-specific expression differences between the ascending and descending aorta, identifying five subtypes of vascular smooth muscle cells in the ascending aorta and four in the descending aorta. Differentially expressed genes between major aortic cell types were also identified. Both, VPS8 and UTP11 were found to expressed in all three major aortic cell types – vascular smooth muscle cells, fibroblasts, and endothelial cells. In conclusion, our case-control association analysis identified two promising candidate risk genes for TAAD (VPS8 and UTP11), warranting further investigation and confirmation in additional cohorts of patients with aortopathy.

Proteome turnover, the process by which proteins are continuously synthesized and degraded, is a crucial biological process for gene expression regulation, cell state maintenance, cellular homeostasis, and response to stimuli. This dissertation outlines novel methods to quantify proteome turnover in both mouse-derived organoid disease models and in vivo using stable isotope labeling combined with mass spectrometry-based methods. In Chapter 1, we review recent LC-MS/MS techniques for measuring proteome turnover, highlighting their applications and limitations. Chapter 2 focuses on a systematic analysis of proteome turnover in an organoid model of pancreatic ductal adenocarcinoma (PDA) using dynamic Stable Isotope Labeling of Organoids (dSILO). This study reveals faster proteome turnover in metastatic organoids compared to primary tumors and identifies several differentially regulated protein complexes in metastatic tumors, particularly from the mitochondrial respiratory chain. In Chapter 3, we present the exploration of various methods for quantifying in vivo proteome turnover in mice. We employed an isotopic pulse-labeling strategy, dynamic Stable Isotopic Labeling of Mammals (dSILAM), then compared four combinations of mass spectrometry-based data acquisition and half-life modeling methods. We uncovered moderate differences in coverage, reproducibility, and half-life estimations between datasets, although further optimization is required for robust conclusions. Chapter 4 discusses potential limitations and future directions for all of the work described herein. Overall, our findings contribute to the optimization of proteomic workflows for studying protein turnover, which can be applied to enhance our understanding of cellular physiology and the molecular mechanisms underlying disease.